Hello, Bwa-mem2 is presented in toolshed for local Galaxy install, but I cannot find it`s data manager to build indexes. How can I start bwa-mem2 on local Galaxy?
Thank you.
The tool itself (bwa-mem2) can build an index from a fasta in your history. If you want prebuilt indeces you can mount our distributed filesystem – Hands-on: Hands-on: Reference Data with CVMFS without Ansible / Galaxy Server administration
You can also put those indeces in data tables by hand.
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Problem was solved in such a way:
- Install bwa-mem2 just as independent conda package in linux environment and build indexes. You should have such a files for HG19 genome:
hg19.fa.pac
hg19.fa.bwt.2bit.64
hg19.fa.ann
hg19.fa.amb
hg19.fa.0123
hg19.fa
Put this file in directory accessible for galaxy and edit/create bwa_mem2_index.loc in the same manner as it is for bwa-mem.
I needed to restart not only galaxy, but all server because of some hunged galaxy tasks from the past.
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